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Blue Collar Bioinformatics (bcbio) is community-developed variant calling, RNA-seq and small RNA analysis. Rapid improvements in high throughput sequencing and associated analysis tools requires continuous validation, benchmarking and tuning of analysis infrastructure. All of this development work is pre-competitive and shared across academic labs, start-ups and larger organizations, making it a great space for open, collaborative work. It's the raw input to the important science we want to do: understand diverse populations, characterize disease mechanisms and contribute to treatments.
This blog contains articles related to bcbio development, tool validation and the open source bioinformatics community:
- Validated variant calling for [germline populations]({{ site.url }}/tags/#germline) and [somatic cancer samples]({{ site.url }}/tags/#cancer)
- Valiation of multiple variant types, including [single nucleotide polymorphisms (SNPs) and small insertions/deletions]({{ site.url }}/tags/#small-variants) and [larger structural rearrangements]({{ site.url }}/tags/#structural-variation)
- [Infrastructure development, including Docker containerization and cloud support on Amazon Web Services]({{ site.url }}/tags/#infrastructure)
- [Benchmarking analysis run times across different compute architectures]({{ site.url }}/tags/#benchmarking)
- [The open source community, including meetings and collaborative codefests]({{ site.url }}/tags/#open-source)
- [Older how-to posts, describing smaller bioinformatics analyses]({{ site.url }}/tags/#how-to)
This work is possible thanks to collaborations with our group in the Bioinformatics Core at Harvard T.H. Chan School of Public Health. We appreciate all of our collaborators who understand and support the value of validated, open, community-developed science: